Properly regulated and maintained telomeric DNA is essential for normal genome stability and replication;malfunctioning telomeres are associated with natural aging as well as with a broad spectrum of human diseases including the major killers cancer and heart disease. Although intensive efforts in many labs including our own have led to a reasonably complete reference DNA sequence for most telomeric regions, DNA sequence gaps still exist adjacent to many telomeres. Perhaps more significantly, telomeric and subtelomeric DNA regions exhibit a very high level of structural variation that is likely to impact telomere function but has yet to be characterized in detail. We intend to address these critical gaps in our knowledge of telomeric DNA regions and in our ability to experimentally characterize the role(s) of telomeric DNA in human biology by accomplishing the following three aims: (1) identify and analyze structural variants in distal subtelomeric regions of the human genome, (2) identify and sequence the distal 5 kb of (TTAGGG)n-adjacent subterminal DNA for each telomere allele of multiple unrelated genomes, and (3) develop PCR-based genotyping assays for unique subterminal allelic variant or class of closely-related variants that can be identified. A new resource of clone libraries and associated paired-end reads constructed as part of the Human Structural Variation initiative will be used along with a combination of computational and wet-lab mapping methods to identify and characterize structural variants in distal human subtelomere regions. Terminal fosmids from these libraries will be identified, mapped and used to characterize and sequence (TTAGGG)n-adjacent subterminal DNA. Identification and characterization of telomeric structural variants will close many of the remaining gaps in the human genome sequence, and will in the long term reveal the universe of common germline subterminal allele structures that exist. The global complement of variant subtelomeric alleles in a given individual may have important consequences for expression in gene-rich subtelomeric regions, and could contribute substantially to both natural human phenotypic variation and to disease phenotypes. Creating a database of allele-specific subterminal sequences will help fill a critical gap in our knowledge of telomere structure and its potential impact on length regulation and stability. Appropriately regulated (TTAGGG)n tracts are critical for normal cell function;individual (TTAGGG)n tract lengths in humans are allele-specific and regulated in part by cis-acting subtelomeric elements. The sequence information on subterminal alleles and allelic variants will open new avenues of telomere research and provide novel opportunities for developing PCR-based methods to track subterminal genotypes in populations and measure allele-specific telomere lengths. Public Health Relevance: The tips of human chromosomes have a variable stretch of (TTAGGG)n sequence;this sequence and associated proteins act to ensure proper replication of our genetic material and the stability of our chromosomes. Critically short (TTAGGG)n tracts trigger cells to stop dividing or to self-destruct;if they do not, chromosome instability and perhaps cancer ensues. Cells normally lose (TTAGGG)n slowly with age, suggesting a possible role for these sequences in both aging and the increased cancer incidence with age. DNA sequences adjacent to (TTAGGG)n tracts participate in its regulation and are needed to study biological mechanisms which occur at individual telomeres;however, these sequences are variable among humans and not well defined in the current human genome sequence. This project aims to fill a major gap in our knowledge of the content and variability of (TTAGGG)n-adjacent DNA sequences and to enable understanding of how these sequences help to regulate (TTAGGG)n tract length;hence its completion could have a very significant impact on our our ability to understand of aging and age-related diseases, including cancer.